We are using global gene expression profiling approach based on the state-of-the-art microarray technology to profile clinical specimens that are associated with different stages of liver diseases. For example, by comparing liver samples from chronic liver disease patients with varying degrees of risk for developing hepatocellular carcinoma, we have identified a unique signature that may be useful in diagnosing patients with early onset of liver cancer. Several serum proteins have been identified as potential diagnostic markers for HCC that are presented in an early stage or in those negative for alpha fetoprotein. We have also developed a unique molecular signature based on the mRNA gene expression of metastatic primary HCC specimens to predict prognosis and metastasis of HCC patients. Osteopontin was identified as a lead gene in this signature and was found to be critical for the metastatic phenotype of HCC. Since HCC is usually present in inflamed liver, due to fibrosis, cirrhosis and/or chronic hepatitis, we also developed a unique molecular prognostic signature based on mRNA gene expression of the liver microenvironment of HCC patients, and suggested that HCC metastatic propensity may be determined and/or influenced by the local tissue microenvironment. Interestingly, the tumor signature is principally different from that of liver microenvironment. We demonstrated that CSF1 may be responsible for the unique signature presented in the liver microenvironment of metastatic HCC patients. Our studies indicate that a predominant humoral cytokine profile occurs in the metastatic liver milieu and that a shift toward anti-inflammatory/immune-suppressive responses may promote HCC metastases. We have identified five genes that may serve as biomarkers for early onset of HCC, especially for those that are negative for alpha-fetoprotein (AFP). We have also disclosed novel prognostic HCC subtypes, characterized by EpCAM and AFP expression that resemble certain stages of hepatogenesis. We have demonstrated that this classification system may facilitate HCC prognosis by enabling the prediction of pharmacological responses to a unique molecular targeted therapy. Currently, we are exploring the roles of these genes in liver cancer initiation and metastasis, particularly their roles in liver cancer stem cells. Our findings have been extremely fruitful as they may not only offer utilities to patient managements, but also challenge the current paradigm of tumor evolution. Clearly, gene expression profiling has expanded our knowledge of the global changes that occur in liver cancer, and has provided numerous insights into the molecular mechanisms of this disease. In addition, these studies will undoubtedly contribute to the establishment of novel markers with potential diagnostic and prognostic value, as well as potential therapeutic targets for direct clinical intervention.